Multiple sequence alignment - TraesCS2A01G484700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G484700 chr2A 100.000 4369 0 0 1 4369 719720129 719724497 0.000000e+00 8069.0
1 TraesCS2A01G484700 chr2A 79.164 1483 176 77 620 2043 751384034 751382626 0.000000e+00 904.0
2 TraesCS2A01G484700 chr2A 96.617 266 8 1 3833 4098 651904145 651904409 1.440000e-119 440.0
3 TraesCS2A01G484700 chr2A 80.876 434 38 20 2977 3375 751381710 751381287 2.550000e-77 300.0
4 TraesCS2A01G484700 chr2A 86.875 160 13 7 2390 2545 751382253 751382098 5.810000e-39 172.0
5 TraesCS2A01G484700 chr2A 75.556 405 46 37 3448 3823 751381182 751380802 2.720000e-32 150.0
6 TraesCS2A01G484700 chr2D 93.447 1816 68 21 2048 3835 585680999 585682791 0.000000e+00 2647.0
7 TraesCS2A01G484700 chr2D 92.436 1613 60 17 496 2047 585679241 585680852 0.000000e+00 2246.0
8 TraesCS2A01G484700 chr2D 80.769 1430 155 71 645 2026 619711928 619710571 0.000000e+00 1007.0
9 TraesCS2A01G484700 chr2D 90.636 566 29 6 1 543 585678677 585679241 0.000000e+00 730.0
10 TraesCS2A01G484700 chr2D 97.015 201 6 0 4169 4369 585682849 585683049 5.410000e-89 339.0
11 TraesCS2A01G484700 chr2D 74.439 1025 125 86 2904 3823 619709697 619708705 9.120000e-82 315.0
12 TraesCS2A01G484700 chr2D 85.366 164 12 8 2390 2545 619710171 619710012 4.520000e-35 159.0
13 TraesCS2A01G484700 chr2D 98.000 50 1 0 4097 4146 585682798 585682847 2.160000e-13 87.9
14 TraesCS2A01G484700 chr2D 86.420 81 6 4 396 472 468866618 468866539 2.800000e-12 84.2
15 TraesCS2A01G484700 chr2B 90.689 1858 65 47 2048 3829 706725619 706727444 0.000000e+00 2374.0
16 TraesCS2A01G484700 chr2B 92.037 1532 57 14 563 2049 706724080 706725591 0.000000e+00 2093.0
17 TraesCS2A01G484700 chr2B 79.001 1681 186 85 645 2237 759450865 759449264 0.000000e+00 994.0
18 TraesCS2A01G484700 chr2B 93.462 413 21 5 23 429 706723353 706723765 3.740000e-170 608.0
19 TraesCS2A01G484700 chr2B 97.512 201 5 0 4169 4369 706727508 706727708 1.160000e-90 344.0
20 TraesCS2A01G484700 chr2B 79.845 516 51 27 2904 3375 759448629 759448123 1.170000e-85 327.0
21 TraesCS2A01G484700 chr2B 79.288 309 35 18 3513 3804 759447951 759447655 5.770000e-44 189.0
22 TraesCS2A01G484700 chr2B 85.276 163 14 7 2390 2545 759449094 759448935 4.520000e-35 159.0
23 TraesCS2A01G484700 chr2B 93.671 79 5 0 463 541 706723771 706723849 7.680000e-23 119.0
24 TraesCS2A01G484700 chr2B 98.000 50 1 0 4097 4146 706727457 706727506 2.160000e-13 87.9
25 TraesCS2A01G484700 chr4A 97.348 264 7 0 3831 4094 78157632 78157369 2.400000e-122 449.0
26 TraesCS2A01G484700 chr3A 97.338 263 7 0 3832 4094 234262846 234263108 8.620000e-122 448.0
27 TraesCS2A01G484700 chr3A 95.911 269 9 2 3833 4101 517388078 517388344 6.710000e-118 435.0
28 TraesCS2A01G484700 chr7A 97.328 262 7 0 3833 4094 506291583 506291322 3.100000e-121 446.0
29 TraesCS2A01G484700 chr7A 95.588 272 10 2 3822 4093 108819689 108819420 6.710000e-118 435.0
30 TraesCS2A01G484700 chr1A 96.958 263 8 0 3832 4094 447114351 447114613 4.010000e-120 442.0
31 TraesCS2A01G484700 chr1A 95.941 271 10 1 3824 4093 62255983 62255713 5.190000e-119 438.0
32 TraesCS2A01G484700 chr6A 95.588 272 12 0 3828 4099 439230808 439231079 1.870000e-118 436.0
33 TraesCS2A01G484700 chr7B 92.958 71 3 2 396 466 18081208 18081140 7.730000e-18 102.0
34 TraesCS2A01G484700 chr4D 90.909 77 5 2 394 469 455925285 455925210 7.730000e-18 102.0
35 TraesCS2A01G484700 chr4D 90.541 74 5 2 393 464 41219426 41219353 3.600000e-16 97.1
36 TraesCS2A01G484700 chr5D 92.537 67 4 1 396 461 63615990 63616056 1.290000e-15 95.3
37 TraesCS2A01G484700 chr5B 87.654 81 5 4 396 471 102640619 102640539 6.020000e-14 89.8
38 TraesCS2A01G484700 chr5B 85.882 85 9 3 383 464 285826253 285826169 2.160000e-13 87.9
39 TraesCS2A01G484700 chr1D 89.041 73 6 2 396 466 319928446 319928518 6.020000e-14 89.8
40 TraesCS2A01G484700 chr3B 88.158 76 2 2 396 464 708518020 708518095 2.800000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G484700 chr2A 719720129 719724497 4368 False 8069.000000 8069 100.000000 1 4369 1 chr2A.!!$F2 4368
1 TraesCS2A01G484700 chr2A 751380802 751384034 3232 True 381.500000 904 80.617750 620 3823 4 chr2A.!!$R1 3203
2 TraesCS2A01G484700 chr2D 585678677 585683049 4372 False 1209.980000 2647 94.306800 1 4369 5 chr2D.!!$F1 4368
3 TraesCS2A01G484700 chr2D 619708705 619711928 3223 True 493.666667 1007 80.191333 645 3823 3 chr2D.!!$R2 3178
4 TraesCS2A01G484700 chr2B 706723353 706727708 4355 False 937.650000 2374 94.228500 23 4369 6 chr2B.!!$F1 4346
5 TraesCS2A01G484700 chr2B 759447655 759450865 3210 True 417.250000 994 80.852500 645 3804 4 chr2B.!!$R1 3159

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
591 874 0.609131 GCTTGGTTTGCCTCCAGCTA 60.609 55.000 0.00 0.0 44.23 3.32 F
1633 2007 1.337071 GCATGCTGAATGACCCATCAG 59.663 52.381 11.37 0.0 38.57 2.90 F
3132 3997 1.609208 TGCTTGCTCTTTCCCACTTC 58.391 50.000 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2867 0.458260 TTGACCATGCATGCATCTGC 59.542 50.000 30.07 20.41 42.62 4.26 R
3155 4020 0.471617 GGCATGCACTAGGAGATGGT 59.528 55.000 21.36 0.00 0.00 3.55 R
4163 5129 3.003793 GTGGTCAGGTTCAAAAGAGAAGC 59.996 47.826 0.00 0.00 44.18 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
302 309 5.192176 AGATTGTGCAAAACCCAAAACAAT 58.808 33.333 0.00 0.00 0.00 2.71
311 318 7.131565 GCAAAACCCAAAACAATGTCTATTTG 58.868 34.615 2.88 2.88 33.62 2.32
379 387 4.864633 TCATAAAGCATGCACGTCAAAAA 58.135 34.783 21.98 0.00 34.35 1.94
407 415 3.381335 ACCATAATGTACTCCCTCCGTT 58.619 45.455 0.00 0.00 0.00 4.44
419 427 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
429 437 9.398170 CCGTTCCATAATATAAGAGCATTTTTG 57.602 33.333 0.00 0.00 0.00 2.44
454 482 8.783093 TGAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
457 485 6.814954 ATGCTCTTATATTATGGGACGGAT 57.185 37.500 0.00 0.00 0.00 4.18
464 492 7.897030 TCTTATATTATGGGACGGATGGAGTAA 59.103 37.037 0.00 0.00 0.00 2.24
528 602 1.609208 CCCAAGTAGTGCAGTTGCTT 58.391 50.000 0.00 2.19 42.66 3.91
546 620 7.439056 CAGTTGCTTTTCATTGTAATTCTGGTT 59.561 33.333 0.00 0.00 0.00 3.67
572 855 8.040132 TGGTTAATGGCTTTATCAATTCAAAGG 58.960 33.333 6.07 0.00 33.30 3.11
578 861 5.482006 GCTTTATCAATTCAAAGGCTTGGT 58.518 37.500 0.00 0.00 33.30 3.67
580 863 6.427853 GCTTTATCAATTCAAAGGCTTGGTTT 59.572 34.615 0.00 0.00 33.30 3.27
582 865 3.465871 TCAATTCAAAGGCTTGGTTTGC 58.534 40.909 0.00 0.00 35.29 3.68
590 873 1.905354 GCTTGGTTTGCCTCCAGCT 60.905 57.895 0.00 0.00 44.23 4.24
591 874 0.609131 GCTTGGTTTGCCTCCAGCTA 60.609 55.000 0.00 0.00 44.23 3.32
593 876 2.450476 CTTGGTTTGCCTCCAGCTAAT 58.550 47.619 0.00 0.00 44.23 1.73
1348 1665 5.408299 CCTTACATGTGAGTTGTTCGATTCA 59.592 40.000 15.73 0.00 0.00 2.57
1349 1666 4.732285 ACATGTGAGTTGTTCGATTCAC 57.268 40.909 0.00 8.21 40.17 3.18
1352 1669 4.594123 TGTGAGTTGTTCGATTCACCTA 57.406 40.909 11.36 0.00 39.27 3.08
1355 1686 3.259902 GAGTTGTTCGATTCACCTACCC 58.740 50.000 0.00 0.00 0.00 3.69
1611 1985 2.027073 GAGCCACATGAACGCGTCA 61.027 57.895 14.44 13.24 41.67 4.35
1633 2007 1.337071 GCATGCTGAATGACCCATCAG 59.663 52.381 11.37 0.00 38.57 2.90
1641 2015 5.828747 CTGAATGACCCATCAGCAAATAAG 58.171 41.667 0.00 0.00 38.57 1.73
1696 2091 3.315142 GATCACCACCGCCAGCAGA 62.315 63.158 0.00 0.00 0.00 4.26
1746 2144 2.962569 CTCCTGTCGCCGAACTCA 59.037 61.111 0.00 0.00 0.00 3.41
1774 2172 3.891586 TTCCAGTCGTCGTCGCTGC 62.892 63.158 16.25 0.00 38.67 5.25
1796 2194 2.439104 GGAGCCTCTTGGAGCCGAT 61.439 63.158 0.00 0.00 34.57 4.18
1893 2297 1.671850 CCGCTACAGTTCACCAACGAT 60.672 52.381 0.00 0.00 37.61 3.73
2073 2631 5.874810 GCATGGAGTAGACAATAACACAAGA 59.125 40.000 0.00 0.00 0.00 3.02
2076 2634 7.724305 TGGAGTAGACAATAACACAAGAAAC 57.276 36.000 0.00 0.00 0.00 2.78
2077 2635 7.506114 TGGAGTAGACAATAACACAAGAAACT 58.494 34.615 0.00 0.00 0.00 2.66
2282 2862 7.175347 ACATACCTATGTATCTACCATGCAG 57.825 40.000 0.00 0.00 44.54 4.41
2283 2863 6.954102 ACATACCTATGTATCTACCATGCAGA 59.046 38.462 0.00 0.00 44.54 4.26
2284 2864 7.454694 ACATACCTATGTATCTACCATGCAGAA 59.545 37.037 0.00 0.00 44.54 3.02
2285 2865 6.942163 ACCTATGTATCTACCATGCAGAAT 57.058 37.500 0.00 0.00 0.00 2.40
2286 2866 7.321717 ACCTATGTATCTACCATGCAGAATT 57.678 36.000 0.00 0.00 0.00 2.17
2287 2867 7.164122 ACCTATGTATCTACCATGCAGAATTG 58.836 38.462 0.00 0.00 0.00 2.32
2345 2971 2.162608 TGGTTGTTTCAAACTCCACACG 59.837 45.455 11.79 0.00 33.67 4.49
2365 3017 2.029486 CGCATTATTTGGTGCATGTTGC 59.971 45.455 0.00 0.00 45.29 4.17
2515 3196 2.633488 GGAAAGGTAATCAAGCGAGCT 58.367 47.619 0.00 0.00 0.00 4.09
2516 3197 2.352960 GGAAAGGTAATCAAGCGAGCTG 59.647 50.000 0.00 0.00 0.00 4.24
2578 3328 5.177327 CCAATGTGCATTACTCAAACCAAAC 59.823 40.000 0.00 0.00 0.00 2.93
2597 3347 5.009210 CCAAACGTCCAAGGAGTTTATGAAA 59.991 40.000 12.88 0.00 36.46 2.69
2649 3404 3.689347 CTTGGAAGTTGGATCCACATCA 58.311 45.455 15.91 6.16 46.37 3.07
2650 3405 4.275810 CTTGGAAGTTGGATCCACATCAT 58.724 43.478 15.91 0.84 46.37 2.45
2651 3406 5.439721 CTTGGAAGTTGGATCCACATCATA 58.560 41.667 15.91 0.00 46.37 2.15
2652 3407 5.651612 TGGAAGTTGGATCCACATCATAT 57.348 39.130 15.91 0.00 41.98 1.78
2653 3408 6.762077 TGGAAGTTGGATCCACATCATATA 57.238 37.500 15.91 0.00 41.98 0.86
2654 3409 7.333779 TGGAAGTTGGATCCACATCATATAT 57.666 36.000 15.91 0.00 41.98 0.86
2655 3410 8.448068 TGGAAGTTGGATCCACATCATATATA 57.552 34.615 15.91 0.00 41.98 0.86
2656 3411 9.061252 TGGAAGTTGGATCCACATCATATATAT 57.939 33.333 15.91 0.00 41.98 0.86
3132 3997 1.609208 TGCTTGCTCTTTCCCACTTC 58.391 50.000 0.00 0.00 0.00 3.01
3151 4016 2.296792 TCCCATTGCCACATGAATACG 58.703 47.619 0.00 0.00 0.00 3.06
3152 4017 2.092699 TCCCATTGCCACATGAATACGA 60.093 45.455 0.00 0.00 0.00 3.43
3153 4018 2.687425 CCCATTGCCACATGAATACGAA 59.313 45.455 0.00 0.00 0.00 3.85
3154 4019 3.318839 CCCATTGCCACATGAATACGAAT 59.681 43.478 0.00 0.00 0.00 3.34
3155 4020 4.518590 CCCATTGCCACATGAATACGAATA 59.481 41.667 0.00 0.00 0.00 1.75
3375 4267 2.418334 GGCCAGTTTAGGTAGACGAAGG 60.418 54.545 0.00 0.00 0.00 3.46
3377 4269 2.496470 CCAGTTTAGGTAGACGAAGGCT 59.504 50.000 0.00 0.00 0.00 4.58
3435 4372 1.079405 GGCGTTCCTCGATCAACCA 60.079 57.895 0.00 0.00 42.86 3.67
3622 4572 1.410882 CTAAGGGACCAGCTAGCTGAC 59.589 57.143 40.03 30.88 46.30 3.51
3692 4648 3.340034 GTTCGTATGATTGGTGGGTTCA 58.660 45.455 0.00 0.00 0.00 3.18
3755 4719 9.968743 GTGTCTAAGAACTAATTTAATGGTTCG 57.031 33.333 13.85 5.47 41.72 3.95
3829 4795 7.819900 AGGTTTCATTCTCTACGGATATATTGC 59.180 37.037 0.00 0.00 0.00 3.56
3835 4801 7.997773 TTCTCTACGGATATATTGCAGTACT 57.002 36.000 0.00 0.00 0.00 2.73
3836 4802 7.612668 TCTCTACGGATATATTGCAGTACTC 57.387 40.000 0.00 0.00 0.00 2.59
3837 4803 6.598457 TCTCTACGGATATATTGCAGTACTCC 59.402 42.308 8.76 8.76 0.00 3.85
3838 4804 4.803098 ACGGATATATTGCAGTACTCCC 57.197 45.455 11.76 4.21 0.00 4.30
3840 4806 4.463186 ACGGATATATTGCAGTACTCCCTC 59.537 45.833 11.76 0.00 0.00 4.30
3841 4807 4.142138 CGGATATATTGCAGTACTCCCTCC 60.142 50.000 11.76 4.95 0.00 4.30
3842 4808 4.142138 GGATATATTGCAGTACTCCCTCCG 60.142 50.000 7.94 0.00 0.00 4.63
3843 4809 2.154567 TATTGCAGTACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
3844 4810 1.276622 ATTGCAGTACTCCCTCCGTT 58.723 50.000 0.00 0.00 0.00 4.44
3845 4811 1.053424 TTGCAGTACTCCCTCCGTTT 58.947 50.000 0.00 0.00 0.00 3.60
3846 4812 1.053424 TGCAGTACTCCCTCCGTTTT 58.947 50.000 0.00 0.00 0.00 2.43
3847 4813 1.418637 TGCAGTACTCCCTCCGTTTTT 59.581 47.619 0.00 0.00 0.00 1.94
3848 4814 2.633967 TGCAGTACTCCCTCCGTTTTTA 59.366 45.455 0.00 0.00 0.00 1.52
3849 4815 3.262405 TGCAGTACTCCCTCCGTTTTTAT 59.738 43.478 0.00 0.00 0.00 1.40
3850 4816 4.259356 GCAGTACTCCCTCCGTTTTTATT 58.741 43.478 0.00 0.00 0.00 1.40
3851 4817 4.698780 GCAGTACTCCCTCCGTTTTTATTT 59.301 41.667 0.00 0.00 0.00 1.40
3852 4818 5.876460 GCAGTACTCCCTCCGTTTTTATTTA 59.124 40.000 0.00 0.00 0.00 1.40
3853 4819 6.036844 GCAGTACTCCCTCCGTTTTTATTTAG 59.963 42.308 0.00 0.00 0.00 1.85
3854 4820 7.101700 CAGTACTCCCTCCGTTTTTATTTAGT 58.898 38.462 0.00 0.00 0.00 2.24
3855 4821 7.605309 CAGTACTCCCTCCGTTTTTATTTAGTT 59.395 37.037 0.00 0.00 0.00 2.24
3856 4822 7.821359 AGTACTCCCTCCGTTTTTATTTAGTTC 59.179 37.037 0.00 0.00 0.00 3.01
3857 4823 5.640783 ACTCCCTCCGTTTTTATTTAGTTCG 59.359 40.000 0.00 0.00 0.00 3.95
3858 4824 4.392754 TCCCTCCGTTTTTATTTAGTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
3859 4825 4.154556 CCCTCCGTTTTTATTTAGTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
3860 4826 5.163693 CCCTCCGTTTTTATTTAGTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
3861 4827 6.037391 CCCTCCGTTTTTATTTAGTTCGCATA 59.963 38.462 0.00 0.00 0.00 3.14
3862 4828 7.255001 CCCTCCGTTTTTATTTAGTTCGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
3863 4829 8.126700 CCTCCGTTTTTATTTAGTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
3874 4840 7.908827 TTAGTTCGCATATTAACTTTGGTCA 57.091 32.000 0.00 0.00 37.19 4.02
3875 4841 6.811253 AGTTCGCATATTAACTTTGGTCAA 57.189 33.333 0.00 0.00 32.00 3.18
3876 4842 7.209471 AGTTCGCATATTAACTTTGGTCAAA 57.791 32.000 0.00 0.00 32.00 2.69
3889 4855 5.890334 CTTTGGTCAAAGTCAAGCTTTACA 58.110 37.500 13.07 0.00 44.95 2.41
3890 4856 5.906113 TTGGTCAAAGTCAAGCTTTACAA 57.094 34.783 13.07 0.00 44.95 2.41
3891 4857 5.906113 TGGTCAAAGTCAAGCTTTACAAA 57.094 34.783 13.07 0.00 44.95 2.83
3892 4858 5.646606 TGGTCAAAGTCAAGCTTTACAAAC 58.353 37.500 13.07 5.27 44.95 2.93
3893 4859 5.417580 TGGTCAAAGTCAAGCTTTACAAACT 59.582 36.000 13.07 2.11 44.95 2.66
3894 4860 6.071616 TGGTCAAAGTCAAGCTTTACAAACTT 60.072 34.615 13.07 7.60 44.95 2.66
3895 4861 6.811665 GGTCAAAGTCAAGCTTTACAAACTTT 59.188 34.615 13.07 12.29 44.95 2.66
3898 4864 7.812309 AAAGTCAAGCTTTACAAACTTTGAC 57.188 32.000 13.07 6.64 44.90 3.18
3899 4865 5.891451 AGTCAAGCTTTACAAACTTTGACC 58.109 37.500 13.07 0.00 0.00 4.02
3900 4866 5.417580 AGTCAAGCTTTACAAACTTTGACCA 59.582 36.000 13.07 0.00 0.00 4.02
3901 4867 6.071616 AGTCAAGCTTTACAAACTTTGACCAA 60.072 34.615 13.07 0.00 0.00 3.67
3902 4868 6.588373 GTCAAGCTTTACAAACTTTGACCAAA 59.412 34.615 8.55 4.99 0.00 3.28
3903 4869 7.277760 GTCAAGCTTTACAAACTTTGACCAAAT 59.722 33.333 8.55 0.00 0.00 2.32
3904 4870 7.821846 TCAAGCTTTACAAACTTTGACCAAATT 59.178 29.630 8.55 0.00 0.00 1.82
3905 4871 8.450180 CAAGCTTTACAAACTTTGACCAAATTT 58.550 29.630 8.55 0.00 0.00 1.82
3906 4872 9.660180 AAGCTTTACAAACTTTGACCAAATTTA 57.340 25.926 8.55 0.00 0.00 1.40
3907 4873 9.830975 AGCTTTACAAACTTTGACCAAATTTAT 57.169 25.926 8.55 0.00 0.00 1.40
4039 5005 9.545105 TTCTATAAACTTGGTCAAACTTTACGA 57.455 29.630 0.00 0.00 0.00 3.43
4040 5006 9.545105 TCTATAAACTTGGTCAAACTTTACGAA 57.455 29.630 0.00 0.00 0.00 3.85
4044 5010 8.766000 AAACTTGGTCAAACTTTACGAAATTT 57.234 26.923 0.00 0.00 0.00 1.82
4045 5011 7.749539 ACTTGGTCAAACTTTACGAAATTTG 57.250 32.000 0.00 0.00 34.11 2.32
4046 5012 7.540299 ACTTGGTCAAACTTTACGAAATTTGA 58.460 30.769 0.00 0.00 38.42 2.69
4052 5018 8.835467 TCAAACTTTACGAAATTTGACTTCAG 57.165 30.769 0.00 0.00 36.42 3.02
4053 5019 8.455682 TCAAACTTTACGAAATTTGACTTCAGT 58.544 29.630 0.00 0.00 36.42 3.41
4054 5020 8.734030 CAAACTTTACGAAATTTGACTTCAGTC 58.266 33.333 0.00 0.00 44.97 3.51
4069 5035 7.462109 GACTTCAGTCAACTCTAATATGCAG 57.538 40.000 1.86 0.00 44.18 4.41
4070 5036 7.175347 ACTTCAGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
4071 5037 7.264221 ACTTCAGTCAACTCTAATATGCAGAG 58.736 38.462 11.37 11.37 44.28 3.35
4083 5049 9.855361 CTCTAATATGCAGAGTAAATGAAAACG 57.145 33.333 0.00 0.00 35.75 3.60
4084 5050 9.594478 TCTAATATGCAGAGTAAATGAAAACGA 57.406 29.630 0.00 0.00 0.00 3.85
4087 5053 5.356882 TGCAGAGTAAATGAAAACGAAGG 57.643 39.130 0.00 0.00 0.00 3.46
4088 5054 5.060506 TGCAGAGTAAATGAAAACGAAGGA 58.939 37.500 0.00 0.00 0.00 3.36
4089 5055 5.529430 TGCAGAGTAAATGAAAACGAAGGAA 59.471 36.000 0.00 0.00 0.00 3.36
4090 5056 6.080406 GCAGAGTAAATGAAAACGAAGGAAG 58.920 40.000 0.00 0.00 0.00 3.46
4091 5057 6.293462 GCAGAGTAAATGAAAACGAAGGAAGT 60.293 38.462 0.00 0.00 0.00 3.01
4092 5058 7.095355 GCAGAGTAAATGAAAACGAAGGAAGTA 60.095 37.037 0.00 0.00 0.00 2.24
4093 5059 8.221766 CAGAGTAAATGAAAACGAAGGAAGTAC 58.778 37.037 0.00 0.00 0.00 2.73
4094 5060 7.387122 AGAGTAAATGAAAACGAAGGAAGTACC 59.613 37.037 0.00 0.00 39.35 3.34
4095 5061 6.993902 AGTAAATGAAAACGAAGGAAGTACCA 59.006 34.615 0.00 0.00 42.04 3.25
4146 5112 2.289257 TGATTGACCTCAGCAGAGTGTG 60.289 50.000 5.32 0.00 40.40 3.82
4147 5113 1.123077 TTGACCTCAGCAGAGTGTGT 58.877 50.000 5.32 0.00 40.40 3.72
4148 5114 0.676184 TGACCTCAGCAGAGTGTGTC 59.324 55.000 5.32 6.26 40.40 3.67
4149 5115 0.965439 GACCTCAGCAGAGTGTGTCT 59.035 55.000 5.32 0.00 40.40 3.41
4150 5116 1.342819 GACCTCAGCAGAGTGTGTCTT 59.657 52.381 5.32 0.00 40.40 3.01
4151 5117 1.765314 ACCTCAGCAGAGTGTGTCTTT 59.235 47.619 5.32 0.00 40.40 2.52
4152 5118 2.171448 ACCTCAGCAGAGTGTGTCTTTT 59.829 45.455 5.32 0.00 40.40 2.27
4153 5119 2.547211 CCTCAGCAGAGTGTGTCTTTTG 59.453 50.000 5.32 0.00 40.40 2.44
4154 5120 1.942657 TCAGCAGAGTGTGTCTTTTGC 59.057 47.619 0.00 0.00 37.33 3.68
4155 5121 1.945394 CAGCAGAGTGTGTCTTTTGCT 59.055 47.619 0.00 0.00 43.24 3.91
4156 5122 3.133691 CAGCAGAGTGTGTCTTTTGCTA 58.866 45.455 0.00 0.00 41.77 3.49
4157 5123 3.561310 CAGCAGAGTGTGTCTTTTGCTAA 59.439 43.478 0.00 0.00 41.77 3.09
4158 5124 4.214971 CAGCAGAGTGTGTCTTTTGCTAAT 59.785 41.667 0.00 0.00 41.77 1.73
4159 5125 5.409520 CAGCAGAGTGTGTCTTTTGCTAATA 59.590 40.000 0.00 0.00 41.77 0.98
4160 5126 6.093219 CAGCAGAGTGTGTCTTTTGCTAATAT 59.907 38.462 0.00 0.00 41.77 1.28
4161 5127 7.278646 CAGCAGAGTGTGTCTTTTGCTAATATA 59.721 37.037 0.00 0.00 41.77 0.86
4162 5128 7.824289 AGCAGAGTGTGTCTTTTGCTAATATAA 59.176 33.333 0.00 0.00 41.83 0.98
4163 5129 8.119226 GCAGAGTGTGTCTTTTGCTAATATAAG 58.881 37.037 0.00 0.00 35.58 1.73
4164 5130 8.119226 CAGAGTGTGTCTTTTGCTAATATAAGC 58.881 37.037 0.00 0.00 36.80 3.09
4165 5131 8.043710 AGAGTGTGTCTTTTGCTAATATAAGCT 58.956 33.333 0.00 0.00 36.27 3.74
4166 5132 8.567285 AGTGTGTCTTTTGCTAATATAAGCTT 57.433 30.769 3.48 3.48 43.19 3.74
4167 5133 8.669243 AGTGTGTCTTTTGCTAATATAAGCTTC 58.331 33.333 0.00 0.00 43.19 3.86
4343 5309 3.849911 TCGCAGGCATATTCTATACTGC 58.150 45.455 0.00 0.00 45.63 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.764434 TGTGCCCAGTTTTGTTTACTTGA 59.236 39.130 0.00 0.00 0.00 3.02
259 266 6.701145 ATCTCTAGTGATCGAGCAACTTTA 57.299 37.500 4.22 0.00 0.00 1.85
302 309 4.105697 AGTCCCTTTGTTCCCAAATAGACA 59.894 41.667 14.69 0.00 40.95 3.41
311 318 2.236644 GAGACCTAGTCCCTTTGTTCCC 59.763 54.545 0.00 0.00 32.18 3.97
340 348 6.675971 GCTTTATGATCCTATCTCGACTACCG 60.676 46.154 0.00 0.00 40.25 4.02
379 387 5.789535 AGGGAGTACATTATGGTCTTAGGT 58.210 41.667 0.00 0.00 0.00 3.08
429 437 8.237267 CCGTCCCATAATATAAGAGCATTTTTC 58.763 37.037 0.00 0.00 0.00 2.29
441 469 6.955267 TGTTACTCCATCCGTCCCATAATATA 59.045 38.462 0.00 0.00 0.00 0.86
451 479 6.709846 AGTACTAGTATGTTACTCCATCCGTC 59.290 42.308 5.75 0.00 40.14 4.79
528 602 9.703892 CATTAACCAACCAGAATTACAATGAAA 57.296 29.630 0.00 0.00 0.00 2.69
546 620 8.040132 CCTTTGAATTGATAAAGCCATTAACCA 58.960 33.333 0.00 0.00 33.62 3.67
572 855 0.609131 TAGCTGGAGGCAAACCAAGC 60.609 55.000 0.00 0.00 44.79 4.01
1348 1665 1.207791 CTGATCCAGCAAGGGTAGGT 58.792 55.000 0.00 0.00 38.24 3.08
1349 1666 1.207791 ACTGATCCAGCAAGGGTAGG 58.792 55.000 0.00 0.00 38.24 3.18
1352 1669 2.290960 GGTAAACTGATCCAGCAAGGGT 60.291 50.000 0.00 0.00 38.24 4.34
1355 1686 3.274288 GAGGGTAAACTGATCCAGCAAG 58.726 50.000 0.00 0.00 34.37 4.01
1445 1806 5.962433 TCAATTTTAGAGTCACGGGAGTAG 58.038 41.667 0.00 0.00 44.67 2.57
1611 1985 2.029623 GATGGGTCATTCAGCATGCTT 58.970 47.619 19.98 0.00 34.76 3.91
1618 1992 5.735354 GCTTATTTGCTGATGGGTCATTCAG 60.735 44.000 0.00 0.00 32.98 3.02
1696 2091 1.561542 CCCCAGACTGGACAATAGCTT 59.438 52.381 23.77 0.00 40.96 3.74
1701 2099 2.971598 CGCCCCCAGACTGGACAAT 61.972 63.158 23.77 0.00 40.96 2.71
1774 2172 1.521616 GCTCCAAGAGGCTCCTCAG 59.478 63.158 17.40 9.48 44.99 3.35
1878 2282 1.227999 CCGCATCGTTGGTGAACTGT 61.228 55.000 0.00 0.00 0.00 3.55
2010 2414 4.515191 CACAAGCTTACCTTTAGTGCAAGA 59.485 41.667 0.00 0.00 0.00 3.02
2082 2647 8.678593 AAGGTTAACTTATTAGCCAGCTATTC 57.321 34.615 5.42 0.00 42.61 1.75
2088 2653 8.336801 ACAAAGAAGGTTAACTTATTAGCCAG 57.663 34.615 5.42 0.00 42.61 4.85
2287 2867 0.458260 TTGACCATGCATGCATCTGC 59.542 50.000 30.07 20.41 42.62 4.26
2288 2868 1.749063 AGTTGACCATGCATGCATCTG 59.251 47.619 30.07 24.30 33.90 2.90
2289 2869 2.139323 AGTTGACCATGCATGCATCT 57.861 45.000 30.07 19.40 33.90 2.90
2290 2870 2.953466 AAGTTGACCATGCATGCATC 57.047 45.000 30.07 20.38 33.90 3.91
2329 2955 2.774439 ATGCGTGTGGAGTTTGAAAC 57.226 45.000 0.00 0.00 0.00 2.78
2345 2971 2.029486 CGCAACATGCACCAAATAATGC 59.971 45.455 2.99 0.00 45.36 3.56
2365 3017 8.600625 CATATATAATACGGGTTTTGATCCACG 58.399 37.037 0.00 0.00 0.00 4.94
2526 3207 4.917385 TGGACATGAAAAGCCTAGCTAAA 58.083 39.130 0.00 0.00 38.25 1.85
2578 3328 8.673711 TGATATTTTTCATAAACTCCTTGGACG 58.326 33.333 0.00 0.00 0.00 4.79
2597 3347 9.959721 ACTCTACTGGTTTGTGTAATGATATTT 57.040 29.630 0.00 0.00 0.00 1.40
2850 3624 3.118738 GGTCGTGGAGGAACTTGATGTAT 60.119 47.826 0.00 0.00 41.55 2.29
3132 3997 2.296792 TCGTATTCATGTGGCAATGGG 58.703 47.619 0.00 0.00 0.00 4.00
3151 4016 3.999663 GCATGCACTAGGAGATGGTATTC 59.000 47.826 14.21 0.00 0.00 1.75
3152 4017 3.244700 GGCATGCACTAGGAGATGGTATT 60.245 47.826 21.36 0.00 0.00 1.89
3153 4018 2.304180 GGCATGCACTAGGAGATGGTAT 59.696 50.000 21.36 0.00 0.00 2.73
3154 4019 1.694150 GGCATGCACTAGGAGATGGTA 59.306 52.381 21.36 0.00 0.00 3.25
3155 4020 0.471617 GGCATGCACTAGGAGATGGT 59.528 55.000 21.36 0.00 0.00 3.55
3377 4269 4.668118 GTTCGTTCCACCCGGCGA 62.668 66.667 9.30 0.00 0.00 5.54
3622 4572 8.146412 TGATCACTATGACATAATTCAGTCCTG 58.854 37.037 0.00 0.00 33.89 3.86
3692 4648 4.955450 TGCAAGCCTAACAACCAATCATAT 59.045 37.500 0.00 0.00 0.00 1.78
3755 4719 5.751990 CCATCACGTACTGGATTAAAGTACC 59.248 44.000 9.43 0.00 44.71 3.34
3829 4795 7.101700 ACTAAATAAAAACGGAGGGAGTACTG 58.898 38.462 0.00 0.00 0.00 2.74
3835 4801 4.392754 GCGAACTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
3836 4802 4.154556 TGCGAACTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
3837 4803 5.285798 TGCGAACTAAATAAAAACGGAGG 57.714 39.130 0.00 0.00 0.00 4.30
3848 4814 8.952278 TGACCAAAGTTAATATGCGAACTAAAT 58.048 29.630 0.00 0.00 34.81 1.40
3849 4815 8.325421 TGACCAAAGTTAATATGCGAACTAAA 57.675 30.769 0.00 0.00 34.81 1.85
3850 4816 7.908827 TGACCAAAGTTAATATGCGAACTAA 57.091 32.000 0.00 0.00 34.81 2.24
3851 4817 7.908827 TTGACCAAAGTTAATATGCGAACTA 57.091 32.000 0.00 0.00 34.81 2.24
3852 4818 6.811253 TTGACCAAAGTTAATATGCGAACT 57.189 33.333 0.00 0.00 37.50 3.01
3853 4819 7.492614 CTTTGACCAAAGTTAATATGCGAAC 57.507 36.000 12.91 0.00 42.02 3.95
3868 4834 7.524698 AAGTTTGTAAAGCTTGACTTTGACCAA 60.525 33.333 15.19 0.00 45.94 3.67
3869 4835 6.071616 AAGTTTGTAAAGCTTGACTTTGACCA 60.072 34.615 15.19 0.00 45.94 4.02
3870 4836 6.330278 AAGTTTGTAAAGCTTGACTTTGACC 58.670 36.000 15.19 0.00 45.94 4.02
3881 4847 9.830975 ATAAATTTGGTCAAAGTTTGTAAAGCT 57.169 25.926 15.08 8.92 39.89 3.74
4013 4979 9.545105 TCGTAAAGTTTGACCAAGTTTATAGAA 57.455 29.630 0.00 0.00 40.73 2.10
4014 4980 9.545105 TTCGTAAAGTTTGACCAAGTTTATAGA 57.455 29.630 0.00 4.22 40.73 1.98
4018 4984 9.857957 AAATTTCGTAAAGTTTGACCAAGTTTA 57.142 25.926 0.00 0.00 38.68 2.01
4019 4985 8.652463 CAAATTTCGTAAAGTTTGACCAAGTTT 58.348 29.630 0.00 0.00 41.89 2.66
4020 4986 8.030106 TCAAATTTCGTAAAGTTTGACCAAGTT 58.970 29.630 0.00 0.00 42.62 2.66
4021 4987 7.540299 TCAAATTTCGTAAAGTTTGACCAAGT 58.460 30.769 0.00 0.00 42.62 3.16
4022 4988 7.979115 TCAAATTTCGTAAAGTTTGACCAAG 57.021 32.000 0.00 0.00 42.62 3.61
4027 4993 8.455682 ACTGAAGTCAAATTTCGTAAAGTTTGA 58.544 29.630 0.00 5.15 44.20 2.69
4028 4994 8.614994 ACTGAAGTCAAATTTCGTAAAGTTTG 57.385 30.769 0.00 1.14 41.14 2.93
4029 4995 8.836959 GACTGAAGTCAAATTTCGTAAAGTTT 57.163 30.769 5.58 0.00 44.18 2.66
4045 5011 7.261325 TCTGCATATTAGAGTTGACTGAAGTC 58.739 38.462 3.41 3.41 44.97 3.01
4046 5012 7.175347 TCTGCATATTAGAGTTGACTGAAGT 57.825 36.000 0.00 0.00 0.00 3.01
4047 5013 7.697352 CTCTGCATATTAGAGTTGACTGAAG 57.303 40.000 5.84 0.00 37.48 3.02
4057 5023 9.855361 CGTTTTCATTTACTCTGCATATTAGAG 57.145 33.333 10.74 10.74 45.59 2.43
4058 5024 9.594478 TCGTTTTCATTTACTCTGCATATTAGA 57.406 29.630 0.00 0.00 0.00 2.10
4061 5027 8.184192 CCTTCGTTTTCATTTACTCTGCATATT 58.816 33.333 0.00 0.00 0.00 1.28
4062 5028 7.552687 TCCTTCGTTTTCATTTACTCTGCATAT 59.447 33.333 0.00 0.00 0.00 1.78
4063 5029 6.876789 TCCTTCGTTTTCATTTACTCTGCATA 59.123 34.615 0.00 0.00 0.00 3.14
4064 5030 5.705441 TCCTTCGTTTTCATTTACTCTGCAT 59.295 36.000 0.00 0.00 0.00 3.96
4065 5031 5.060506 TCCTTCGTTTTCATTTACTCTGCA 58.939 37.500 0.00 0.00 0.00 4.41
4066 5032 5.607119 TCCTTCGTTTTCATTTACTCTGC 57.393 39.130 0.00 0.00 0.00 4.26
4067 5033 7.190920 ACTTCCTTCGTTTTCATTTACTCTG 57.809 36.000 0.00 0.00 0.00 3.35
4068 5034 7.387122 GGTACTTCCTTCGTTTTCATTTACTCT 59.613 37.037 0.00 0.00 0.00 3.24
4069 5035 7.172019 TGGTACTTCCTTCGTTTTCATTTACTC 59.828 37.037 0.00 0.00 37.07 2.59
4070 5036 6.993902 TGGTACTTCCTTCGTTTTCATTTACT 59.006 34.615 0.00 0.00 37.07 2.24
4071 5037 7.193377 TGGTACTTCCTTCGTTTTCATTTAC 57.807 36.000 0.00 0.00 37.07 2.01
4072 5038 7.804843 TTGGTACTTCCTTCGTTTTCATTTA 57.195 32.000 0.00 0.00 37.07 1.40
4073 5039 6.702716 TTGGTACTTCCTTCGTTTTCATTT 57.297 33.333 0.00 0.00 37.07 2.32
4074 5040 6.702716 TTTGGTACTTCCTTCGTTTTCATT 57.297 33.333 0.00 0.00 37.07 2.57
4075 5041 6.894339 ATTTGGTACTTCCTTCGTTTTCAT 57.106 33.333 0.00 0.00 37.07 2.57
4076 5042 6.319152 TCAATTTGGTACTTCCTTCGTTTTCA 59.681 34.615 0.00 0.00 37.07 2.69
4077 5043 6.731164 TCAATTTGGTACTTCCTTCGTTTTC 58.269 36.000 0.00 0.00 37.07 2.29
4078 5044 6.702716 TCAATTTGGTACTTCCTTCGTTTT 57.297 33.333 0.00 0.00 37.07 2.43
4079 5045 6.894339 ATCAATTTGGTACTTCCTTCGTTT 57.106 33.333 0.00 0.00 37.07 3.60
4080 5046 6.894339 AATCAATTTGGTACTTCCTTCGTT 57.106 33.333 0.00 0.00 37.07 3.85
4081 5047 7.989416 TTAATCAATTTGGTACTTCCTTCGT 57.011 32.000 0.00 0.00 37.07 3.85
4089 5055 9.869757 GCCACTTTTATTAATCAATTTGGTACT 57.130 29.630 0.00 0.00 0.00 2.73
4090 5056 9.646427 TGCCACTTTTATTAATCAATTTGGTAC 57.354 29.630 0.00 0.00 0.00 3.34
4092 5058 9.382275 GATGCCACTTTTATTAATCAATTTGGT 57.618 29.630 0.00 0.00 0.00 3.67
4093 5059 9.603921 AGATGCCACTTTTATTAATCAATTTGG 57.396 29.630 0.00 0.00 0.00 3.28
4152 5118 8.893727 GGTTCAAAAGAGAAGCTTATATTAGCA 58.106 33.333 15.59 0.00 43.68 3.49
4163 5129 3.003793 GTGGTCAGGTTCAAAAGAGAAGC 59.996 47.826 0.00 0.00 44.18 3.86
4164 5130 4.199310 TGTGGTCAGGTTCAAAAGAGAAG 58.801 43.478 0.00 0.00 0.00 2.85
4165 5131 4.229304 TGTGGTCAGGTTCAAAAGAGAA 57.771 40.909 0.00 0.00 0.00 2.87
4166 5132 3.924114 TGTGGTCAGGTTCAAAAGAGA 57.076 42.857 0.00 0.00 0.00 3.10
4167 5133 3.885297 ACATGTGGTCAGGTTCAAAAGAG 59.115 43.478 0.00 0.00 34.88 2.85
4290 5256 3.603532 CATGCCGATAATCCACTAGCAT 58.396 45.455 0.00 0.00 39.92 3.79
4328 5294 5.907197 AACACACGCAGTATAGAATATGC 57.093 39.130 0.00 0.00 41.61 3.14
4343 5309 4.272504 AGACCACATAACAAGAAACACACG 59.727 41.667 0.00 0.00 0.00 4.49


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.